Chlamydia trachomatis is an obligate intracellular human pathogen. Chlamydia infection is a common sexually-transmitted disease and the bacterium can cause numerous disease states in both men and women. Clinical symptoms include urethritis, proctitis, trachoma, infertility, prostatitis, epididymitis, cervicitis, pelvic inflammatory disease (PID) and ectopic pregnancy. It is also a neonatal pathogen where it can cause infection of the eyes and lungs.
Infection with Chlamydia trachomatis is one of the most common sexually transmitted diseases worldwide. It is estimated that 2-3 million individuals in the United States are infected with Chlamydia. In the United Kingdom, it has been estimated that one in ten sexually active young people under 25 are infected with Chlamydia. 
Chlamydia trachomatis infection can be successfully treated by antibiotics, for example, tetracyclines such as doxycycline or acrolides such as azithromycin. In order to ensure that appropriate treatment is given in timely fashion, there is a need to accurately diagnose infection by Chlamydia trachomatis. In some countries such as the UK, a national programme of Chlamydia screening has been launched.
The infectious unit of Chlamydia trachomatis is the elementary body (EB). The EB functions as a “spore-like” body whose purpose is to permit Chlamydial survival in a non-supportive environment outside of the host cell. The EB is thought to be metabolically inert until it attaches to and is endocytosed by a susceptible host cell. Detection of Chlamydia trachomatis is possible by nucleic acid amplification methods, for example, Polymerase Chain Reaction (PCR) based methods. PCR has the potential to amplify nucleic acid from both infected cells and EBs. Chlamydia trachomatis contains genetic material in both its chromosome, which is present as a single copy, and in its plasmid which is present in, 6 to 10 copies per EB. Historically, the plasmid has been used as a preferred target for nucleic acid amplification tests due to its multiple copies per EB and the assumed greater sensitivity obtainable by detecting a plasmid-based target. However, suitability of the plasmid nucleic acid amplification test detection systems has been called into question following the discovery of the Swedish variant of Chlamydia trachomatis. The Swedish variant contains a 377 base pair deletion in the plasmid and therefore detection systems targeted at the deleted region will give a false negative result when confronted with Swedish variant Chlamydia trachomatis. 
The present invention is based on the realisation that an assay detecting sequence present in the Chlamydia trachomatis chromosome is potentially more stable because the chromosomal genes are in general less mutable and because in certain circumstances it may be possible for the plasmid to be lost entirely. Targeting a gene present in the chromosome might be expected to be disadvantageous because chromosomal targets are only present as a single copy per cell. However, the inventors of the present invention were surprised to discover that chromosomal targets are able to provide limits of detection (LOD) comparable to plasmid targets.
Nucleic Acid Amplification Tests (NAATs)
A number of nucleic acid amplification test (NAAT) methods suitable for use with the invention are available. They include the well-known PCR, the ligase chain reaction (LCR), strand displacement amplification (SDA), recombinase-polymerase amplification (RPA), transcription mediated amplification, nucleic acid sequence-based amplification (NASBA), Helicase-dependent amplification and loop-mediated isothermal amplification. NAAT methods have largely displaced culture based detection for C. trachomatis methods not least because culture based methods involved the added complexity of requiring the use of mammalian cell or tissue culture. They involve detecting nucleic acids in a highly sensitive sequence-specific manner involving amplification of one or more target sequences using enzymes.
For further details of NAATs; the reader is referred to the following references which are incorporated by reference:                Nucleic Acid Sequence Based Amplification (NASBA)                    Compton J. Nucleic acid sequence-based amplification Nature 1991:350(6313):91-2                        Transcription Mediated Amplification                    Wroblewski J. et al. Comparison of Transcription. Mediated Amplification and PCR Assay Results from Various Genital Specimen Types for Detection of Mycoplasma genitalium. J. Clin. Microbiol. 2006:44(9):3306-3312                        Ligase Chain Reaction                    Wiedmann M. et al. Ligase chain reaction (LCR) overview and Applications. PCR. Methods and Applications 1994 3(4)S51-64                        Loop-Mediated Isothermal amplification of DNA                    Notomi et al. Loop-Mediated isothermal amplification of DNA. Nucleic Acids. Res. 2000 23 (12):E63.                        Helicase-Dependent Amplification                    Vincent M. et al. Helicase-dependent isothermal DNA Amplification EMBO Rep. 2004 5(8) 795-800                        Strand Displacement amplification                    Strand displacement amplification—an isothermal in vitro Amplification technique. Walker et al. Nucleic Acids Res. 1992. 20(7) 1691-1696                        Recombinase-Polymerase Amplification (RPA)                    DNA Amplification and Detection Made Simple (Relatively). Hoff. M. Public Libr. Sic. 2006: 4(7): e222; and also U.S. Pat. No. 7,270,981.Polymerase Chain Reaction (PCR)                        
PCR is a method of detecting nucleic acids in a highly sensitive sequence-specific manner involving amplification of one or more target sequences by using a thermostable polymerase enzyme and cycling the temperature conditions of the reaction.
In its simplest form a PCR reaction cycles through three stages: i) a denaturation stage occurring at a temperature of approximately 90-100° C. At this elevated temperature double-stranded DNA denatures or “melts” to form single-stranded DNA, ii) primer annealing at a typical temperature of 50-65° C. In this step the forward and reverse primers hybridize to the complimentary regions of any target present in the solution, and iii) extension typically occurring at 50-80° C. during which the polymerase chain reaction utilises deoxynucleotide triphosphates in the solution to extend the 3′ end of the primers. Typically, the cycle is carried out 25-45 times. According to certain PCR protocols the annealing step and the extension step may be conflated so that the sample cycles through a two-step programme of 90° C. to 100° C. then 50° C. to 80° C. intervals. Theoretical calculations show that a 30 cycle PCR reaction can amplify a single target molecule 268,435,456 times. Because of inefficiencies in the amplification reaction, actual amplification may be less than this, but nevertheless the PCR reaction is typically able to amplify single or very low numbers of target molecules millions of times to a level at which they can be much more easily detected. PCR reactions rely on a thermostable DNA polymerase, for example, Taq polymerase isolated from the thermophilic bacterium Thermus aquaticus. Other thermostable DNA polymerases can be used in place of Taq, for example, Pfu polymerase isolated from Pyrococcus furiosus which has a proof-reading activity absent from Taq polymerase and is therefore a higher fidelity enzyme.
A review of the polymerase chain reaction is found in most molecular biology textbooks, see, for example, “Principles of Gene Manipulation—An Introduction to Genetic Engineering” by Old and Primrose, Blackwell Science Ltd which is incorporated herein by reference. There are a number of different “PCR formats”. As a basic requirement, a PCR reaction requires a forward primer and a reverse primer designed to hybridize either side of the target sequence. The amplification reaction occurs in respect of the intervening sequence between the two primers. The detection of amplified PCR products may be carried out in a non-specific way which merely detects the presence of double-stranded nucleic acid (for example, by use of a double-stranded-DNA intercalating dye such as ethidium bromide or SYBR-green). Alternatively, a semi-specific detection of product may be carried out by resolving approximate molecular weight of the product, for example, by Carrying out an electrophoresis of the reaction products prior to detection. Alternatively, there are a number of sequence-specific detection methods which typically involve the hybridization of a sequence-specific nucleic acid probe to the amplified region or which measure the degradation of the probe concomitant with the amplification of the target sequence and make use of the nucleic acid exonuclease activity of the nucleic acid polymerase. PCR-based methods of detection for pathogenic agents typically offer the advantage of faster results than more traditional methods which usually involve culture and incubation over a number of days. A PCR result can be made available in a few hours or less.